CHANGES IN VERSION 5.3
    o  new VCF extract for demonstrating cisAssoc VCF-SummarizedExperiment
       analysis
    o  GGtools kept for legacy/migration purposes only; use gQTLBase and gQTLstats
       instead

CHANGES IN VERSION 4.11
----------------------
    o  appraise and calfig are provided to foster evaluation of
       eQTL-based GWAS hit predictions
    o  cisAssoc has been added to obtain assay data from SummarizedExperiment
       and variants from VCF
    o  CisConfig instances keepMapCache now defaults to TRUE
    o  for naming symmetry we now have cisScores and transScores 
       operating on CisConfig and TransConfig instances respectively
    o  Added transeqByCluster() for nested concurrency for trans searches
    o  Added TransConfig class to control trans searches, and modified
       transScores accordingly
    o  Added hmm878, chromatin map of GM12878 for assessment of chromatin state enrichments
    o  Added gffprocess(), of use when All.cis is used to generate
chunk-specific gff3: gffprocess uses external sort/grep/tabix to
unify the chunks into a single tabix-indexed gff3
    o pifdr() has been changed to avoid approximation on a grid and to
      compute binning of permuted scores more rapidly using hist();
      old behavior recoverable with legacy=TRUE
    o ciseqByCluster() uses nested concurrency to perform cis searches

CHANGES IN VERSION 4.10
----------------------
    o  Sharply revised vignette

CHANGES IN VERSION 4.9
----------------------
    o  All.cis accepts a CisConfig instance to define parameters of a 
	cis search

CHANGES IN VERSION 4.7
----------------------
    o  The snplocsDefault() function has been added to simplify appropriate
       selection of SNPlocs.Hsapiens.dbSNP.* to a common value for all usages

    o  The sensanal() function now operates on a sensiCisInput instance to
       help provide an overview of sensitivity analysis for cis-eQTL searches

CHANGES IN VERSION 4.6
----------------------

    o  The primary tools for one-population analyses are best.cis.eQTLs and
       transScores.  Multipopulation analyses are handled with 
       meta.best.cis.eQTLs and meta.transScores.

    o  High volume genotype data has been addressed by packaging ExpressionSet
       and chromosome-specific SnpMatrix instances; requests for expression
       plus genotype data are directed to packages mediated through 
       GGBase::getSS.

    o  Two species of data filtering parameters that may be used jointly 
       in the primary tools are exFilter, which operates on expression 
       component prior to any analyses, and smFilter, which operates on the
       entire smlSet.  exFilter may be used to isolate samples of interest
       early in the workflow, for example when an expression plus genotype
       package includes samples from distinct tissues on the same individuals.

    o  june 2012: exFilter facility properly handled in best.cis.eQTLs.mchr

    o  may 2012: best.cis.eQTLs has getDFFITS option

    o  march 2010: gwSnpTests and so forth are deprecated in favor
       of simpler interfaces that can be more readily parallelized.  New
       IRanges-based computations for cis restrictions will be introduced


CHANGES IN VERSION 3.0
----------------------

    o  march 2008: complete overhaul to use snpMatrix genotype 
       representation.  gwSnpScreen is main interface

    o  manage warnings of ff.[ a bit better, May 13 2012

    o  racExSet is not a primary tool any more; smlSet is

